Sounds like your transfer switch is acting up. It charged under genset power and when moved to shore it seems to correctly switch to shore only to switch off of shore a couple hours later because maybe it thinks it needs to switch to genset erroneously. That's my guess. I believe your transfer switch is made by
Intellitec and you can get manuals and test info at their web site. A battery boost would not affect the transfer switch.
If you had said it only losses charger capability after a couple hours I might point to the BIRD (also made by Intellitec) which I think your coach will have. It might be possible for a battery boost to partially zap the BIRD causing erratic operation of it, I don't know for sure.